Analytical and Bioanalytical Chemistry

, Volume 404, Issue 4, pp 939–965 | Cite as

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

  • Marcus BantscheffEmail author
  • Simone Lemeer
  • Mikhail M. Savitski
  • Bernhard KusterEmail author


Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.


Quantitative proteomics Liquid chromatography Mass spectrometry Bioinformatics 



Affinity purification


Data-dependent acquisition


Electrospray ionization


Higher-energy collision-induced dissociation


Histone deacetylase


High-pressure liquid chromatography


Inductively coupled plasma


Immobilized metal affinity chromatography


Isobaric tags for absolute and relative quantification


Liquid chromatography


Multiple reaction monitoring


Mass spectrometry


Tandem mass spectrometry


Protein abundance index


Protein epitope signature tag


Protein standard absolute quantification


Peptide-to-spectrum match


Post-translational modification


Quadrupole time of flight


Stable isotope labeling with amino acids in cell culture


Selected reaction monitoring


Tandem mass tag


Ultra-high-pressure liquid chromatography


Extracted ion chromatogram



The authors wish to thank Frank Weissbrodt for help with creating the graphics. We apologize to all authors whose interesting work could not be cited owing to space or conceptual constraints.


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Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  1. 1.Cellzome AGHeidelbergGermany
  2. 2.Chair of Proteomics and BioanalyticsTechnische Universität MünchenFreisingGermany
  3. 3.Center for Integrated Protein Science Munich (CIPSM)MunichGermany

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